Physical Sciences and Mathematics Commons^™

Performance Analysis Of Droughthpc, Yasodhadevi Nachimuthu

Student Research Symposium

We present our performance analysis of DroughtHPC, a software application being developed by an interdisciplinary effort lead by Dr.Moradkhani in the Civil Engineering department, Dr. Daescu in the Math Department, and Dr. Karavanic in the Computer Science Department.

The DroughtHPC application is used to predict drought conditions for a target geographical area. The data used in the prediction are soil conditions, vegetation layers, canopy cover, snow accumulation information from satellites, and meteorological data. DroughtHPC is written in Python and uses two hydrologic models, PRMS [1] and VIC [2], to simulate soil moisture levels. A larger geographical area such as the …

Finite Element Method Analysis Of Resonant Cavity For Whispering Gallery Acoustic Sensing Microscopy, Thanh N.D. Le, Ha Tran, Andres H. La Rosa

Student Research Symposium

Whispering Gallery Acoustic Sensing (WGAS) has been studied by Department of Physics at Portland State University as a mean of controlling sample to probe distance in tuning-folk-based scanning probe microscopy (TF-SPM). WGAS uses the microscope frame as a resonance acoustic cavity. The setup shows high potential because of high-quality factor nature of acoustic cavity as well as using mechanical motions of the TF itself instead of electrical signals. However, the analytic solution of the eigenfrequencies of the current microscope frame is very complex due to the asymmetric geometry. The purpose of this study is to use finite element method to …

Forecasted Range Shifts Of Arid-Land Fishes In Response To Climate Change, James E. Whitney, Joanna B. Whittier, Craig Patrick Paukert, Julian D. Olden, Angela L. Strecker

Environmental Science and Management Faculty Publications and Presentations

Climate change is poised to alter the distributional limits, center, and size of many species. Traits may influence different aspects of range shifts, with trophic generality facilitating shifts at the leading edge, and greater thermal tolerance limiting contractions at the trailing edge. The generality of relationships between traits and range shifts remains ambiguous however, especially for imperiled fishes residing in xeric riverscapes. Our objectives were to quantify contemporary fish distributions in the Lower Colorado River Basin, forecast climate change by 2085 using two general circulation models, and quantify shifts in the limits, center, and size of fish elevational ranges according …

Leed O+M Materials Audit: Blumel Hall, Emily Murkland, Taylor Stone, John Dea, Kristen Purdy

Campus Sustainability Office Publications, Reports and Presentations

• This report provides the Campus Sustainability Office with an objective, third party Materials Audit for Blumel Hall in Portland, Oregon. The data collected for this audit provides Campus Sustainability Office with insight into Blumel’s current waste composition and diversion rate as well as identifies opportunities to improve recycling, composting, and areas for reduction of materials consumption. Community Environmental Services (CES) conducted Materials Audits for 100% of Blumel Hall’s landfill-bound, commingled recycling, glass bottles and jars recycling, and compost streams during a 24-hour period.

Psu Urban Center Building Leed Eb Materials Audit Report, Emily Murkland, Taylor Stone, John Dea, Kristen Purdy

Campus Sustainability Office Publications, Reports and Presentations

This report provides the Campus Sustainability Office with an objective, third party Materials Audit for Portland State University’s Urban Center Building in Portland, Oregon. The data collected for this audit provides Campus Sustainability Office with insight into Urban Center’s current waste composition and diversion rate as well as identifies opportunities to improve recycling, composting, and areas for reduction of materials consumption. Community Environmental Services (CES) conducted materials audits for 100% of Urban Center’s landfill-bound, commingled recycling, glass bottles and jars recycling, and compost streams during a 24-hour period.

The Effect Of Plasma On Graphene Quality In An Inductively Couple Plasma Chemical Vapor Deposition Reactor, Brendan Coyne

Undergraduate Research & Mentoring Program

Despite continued interest in research and application development, full scale graphene production is still limited by many factors including prohibitively high growth temperature requirements. Extremely high quality graphene growth is possible at high temperatures using chemical vapor deposition (CVD). Use of an inductively coupled plasma chemical vapor deposition (ICP CVD) reactor with the benefit of precursor gas decomposition through plasma generation, may provide possibility to reduce growth temperature. Herein, we report plasma’s effects on graphene growth by comparing growths of increasing power supplied to plasma generation and changes in precursor gas ratios. Plasma composition was characterized by ultraviolet and visible …

Using An Altimeter-Derived Internal Tide Model To Remove Tides From In Situ Data, Edward D. Zaron, Richard D. Ray

Civil and Environmental Engineering Faculty Publications and Presentations

Internal waves at tidal frequencies, i.e., the internal tides, are a prominent source of variability in the ocean associated with significant vertical isopycnal displacements and currents. Because the isopycnal displacements are caused by ageostrophic dynamics, they contribute uncertainty to geostrophic transport inferred from vertical profiles in the ocean. Here it is demonstrated that a newly developed model of the main semidiurnal (M2) internal tide derived from satellite altimetry may be used to partially remove the tide from vertical profile data, as measured by the reduction of steric height variance inferred from the profiles. It is further demonstrated that the internal …

Essentials Of Building Virtual Instruments With Labview And Arduino For Lab Automation Applications, Jianghua Bai, Andres H. La Rosa

Physics Faculty Publications and Presentations

Four ways to improve the capabilities of a virtual instrument involving a microcontroller are covered in this paper. They are structural modeling and programming, real-time control, asynchronous communication between the microcontroller and the host PC, and system integration. This paper covers 4 common problems encountered by embedded developers and 5 solutions to the 4 problems. The solutions and examples demonstrated in this article will help readers build robust and reliable virtual instruments for crucial applications.

Environmental Dna (Edna) Detects The Invasive Crayfishes Orconectes Rusticus And Pacifastacus Leniusculus In Large Lakes Of North America, Eric R. Larson, Mark A. Renshaw, Crysta Gantz, John Umek, Sudeep Chandra, David M. Lodge, Scott P. Egan

Environmental Science and Management Faculty Publications and Presentations

We report results of a study that made reciprocal comparisons of environmental DNA (eDNA) assays for two major invasive crayfishes between their disparate invasive ranges in North America. Specifically, we tested for range expansions of the signal crayfish Pacifastacus leniusculus (Dana, 1852) into the Laurentian Great Lakes region known to be invaded by the rusty crayfish Orconectes rusticus (Girard, 1852), as well as for the invasion of O. rusticus into large lakes of California and Nevada, US known to be invaded by P. leniusculus. We compared eDNA detections to historic localities for O. rusticus within the Great Lakes, and to …

Simplified Reversed Chloroquines To Overcome Malaria Resistance To Quinoline-Based Drugs, Bornface Gunsaru, Steven J. Burgess, Westin Morrill, Jane X. Kelly, Shawheen Shomloo, Martin J. Smilkstein, Katherine May Liebman, David H. Peyton

Chemistry Faculty Publications and Presentations

Building on our earlier work of attaching a chemosensitizer (reversal agent) to a known drug pharmacophore, we have now expanded the structure-activity relationship study to include simplified versions of the chemosensitizer. The change from two aromatic rings in this head group to a single ring does not appear to detrimentally affect the antimalarial activity of the compounds. Data from in vitro heme binding and beta-hematin inhibition assays suggest that the single aromatic RCQ compounds retain activities against Plasmodium falciparum similar to those of CQ, although other mechanisms of action may be relevant to their activities.

Continental-Scale Homogenization Of Residential Lawn Plant Communities, Megan M. Wheeler, Christopher Neill, Peter M. Groffman, Meghan Avolio, Neil D. Bettez, Jeannine Cavender-Bares, Rinku Roy Chowdhury, Lindsay Darling, J. Morgan Grove, Sharon J. Hall, James B. Heffernan, Sarah E. Hobbie, Kelli L. Larson, Jennifer L. Morse, Kristen C. Nelson, Laura A. Ogden, Jarlath O'Neil-Dunne, Diane E. Pataki, Colin Polsky, Meredith Steele, Tara Trammell

Environmental Science and Management Faculty Publications and Presentations

Residential lawns are highly managed ecosystems that occur in urbanized landscapes across the United States. Because they are ubiquitous, lawns are good systems in which to study the potential homogenizing effects of urban land use and management together with the continental-scale effects of climate on ecosystem structure and functioning. We hypothesized that similar homeowner preferences and management in residential areas across the United States would lead to low plant species diversity in lawns and relatively homogeneous vegetation across broad geographical regions. We also hypothesized that lawn plant species richness would increase with regional temperature and precipitation due to the presence …

Gas Transfer Velocities In Small Forested Ponds, Meredith A. Holgerson, Emily R. Farr, Peter A. Raymond

Environmental Science and Management Faculty Publications and Presentations

Inland waters actively exchange gases with the atmosphere, and the gas exchange rate informs system biogeochemistry, ecology, and global carbon budgets. Gas exchange in medium- to large-sized lakes is largely regulated by wind; yet less is known about processes regulating gas transfer in small ponds where wind speeds are low. In this study, we determined the gas transfer velocity, k₆₀₀, in four small ( < 250 m² ) ponds by using a propane ( C₃H₈ ) gas injection. When estimated across 12 h periods, the average k₆₀₀ ranged from 0.19 to 0.72 m d^-1 across …

Competition Amplifies Drought Stress In Forests Across Broad Climatic And Compositional Gradients, Kelly E. Gleason, John B. Bradford, Alessandra Bottero, Anthony W. D'Amato, Shawn Fraver, Brian J. Palik, Michael A. Battaglia, Louis Iverson, Laura Kenefic, Christel C. Kern

Environmental Science and Management Faculty Publications and Presentations

Forests around the world are experiencing increasingly severe droughts and elevated competitive intensity due to increased tree density. However, the influence of interactions between drought and competition on forest growth remains poorly understood. Using a unique dataset of stand-scale dendrochronology sampled from 6405 trees, we quantified how annual growth of entire tree populations responds to drought and competition in eight, long-term (multi-decadal), experiments with replicated levels of density (e.g., competitive intensity) arrayed across a broad climatic and compositional gradient. Forest growth (cumulative individual tree growth within a stand) declined during drought, especially during more severe drought in drier climates. Forest …

Evidence For Distributed Clockwise Rotation Of The Crust In The Northwestern United States From Fault Geometries And Focal Mechanisms, Thomas M. Brocher, Ray E. Wells, Andrew P. Lamb, Craig S. Weaver

Geology Faculty Publications and Presentations

Paleomagnetic and GPS data indicate that Washington and Oregon have rotated clockwise for the past 16 Myr. Late Cenozoic and Quaternary fault geometries, seismicity lineaments, and focal mechanisms provide evidence that this rotation is accommodated by north directed thrusting and right-lateral strike-slip faulting in Washington, and SW to W directed normal faulting and right-lateral strike-slip faulting to the east. Several curvilinear NW to NNW trending high-angle strike-slip faults and seismicity lineaments in Washington and NW Oregon define a geologic pole (117.7°W, 47.9°N) of rotation relative to North America. Many faults and focal mechanisms throughout northwestern U.S. and southwestern British Columbia …

Slope, Grain Size, And Roughness Controls On Dry Sediment Transport And Storage On Steep Hillslopes, Roman A. Dibiase, Michael P. Lamb, Vamsi Ganti, Adam M. Booth

Geology Faculty Publications and Presentations

Existing hillslope sediment transport models developed for low-relief, soil-mantled landscapes are poorly suited to explain the coupling between steep rocky hillslopes and headwater channels. Here we address this knowledge gap using a series of field and numerical experiments to inform a particle-based model of sediment transport by dry ravel—a mechanism of granular transport characteristic of steep hillslopes. We find that particle travel distance increases as a function of the ratio of particle diameter to fine-scale (1m) topographic variability associated with rocky landscapes. Applying a 2-D dry-ravel-routing model to lidar-derived surface topography, we show how spatial patterns of local and nonlocal …

Past, Present, And Future Of Ecological Integrity Assessment For Fresh Waters, Lauren M. Kuehne, Julian D. Olden, Angela L. Strecker, Joshua J. Lawler, David M. Theobald

Environmental Science and Management Faculty Publications and Presentations

One of the most influential environmental laws in the US – the 1972 Clean Water Act – included the visionary objective of maintaining and restoring aquatic ecological integrity. However, the efficacy of the Act depends on how integrity is assessed. Reviewing the assessment literature for fresh waters over the past 40 years, we found evidence of methodological trends toward increased repeatability, transferability, and robustness of assessments over time. However, implementation gaps were revealed, based on the relatively weak linkages to freshwater policies, stakeholder involvement, emerging threats, and conservation opportunities. A related survey of assessment practitioners underscored the disparity between need …

Modeling Of Ultrafine Particle Emissions And Ambient Levels For The Near Roadside Environment, Sauda Ahmed

Dissertations and Theses

Various epidemiological studies have linked exposure to Ultrafine Particles (UFP; diameter< 100 nm) to adverse health impacts. Roadway traffic is one of the major sources of UFPs and heavily influences UFP concentrations in the nearby vicinity of major roadways. Modeling efforts to predict UFPs have been limited due to the scarcity of reliable information on emissions, lack of monitoring data and limited understanding of complex processes affecting UFP concentrations near sources.

In this study continuous measurement of ultrafine particle number concentrations (PNC) and mass concentrations of nitric oxide (NO), nitrogen dioxide (NO₂) and PM_2.5 was conducted near an arterial road and freeway at different seasons and meteorological conditions and integrated with traffic count data. PNC showed high correlation with NO (r=0.64 for arterial; 0.61 for freeway), NO2 (r=0.57 for arterial; 0.53 for freeway) and NOx (NOx=NO+NO2; r=0.63 for arterial; 0.59 for freeway) and moderate to low correlation with traffic volume (r=0.33 for arterial; 0.32 for freeway) and …

Advancing Collaborative Solutions: Lessons From The Oregon Sage-Grouse Conservation Partnership (Sagecon), Jennifer H. Allen, Turner Odell, Julia Babcock, Charis Henrie

National Policy Consensus Center Publications and Reports

The Sage-Grouse Conservation Partnership, also known as “SageCon,” was an unprecedented collaborative effort among federal, state, and private stakeholders to address landscape-scale threats to greater sage-grouse while also acknowledging rural economic and community interests across eastern Oregon’s sagebrush range. A U.S. Fish and Wildlife Service (USFWS) preliminary finding that the sage-grouse warranted listing under the endangered species act, and a subsequent court settlement setting a deadline for a final listing decision were key drivers for SageCon participants to seek proactive solutions to protect the bird. A cadre of diverse Eastern Oregon stakeholders with experience working collaboratively on related public lands …

Remote Measurements Of Tides And River Slope Using An Airborne Lidar Instrument, Austin S. Hudson, Stefan A. Talke, Ruth Branch, Chris Chickadel, Gordon Farquharson, Andrew Jessup

Civil and Environmental Engineering Faculty Publications and Presentations

Tides and river slope are fundamental characteristics of estuaries, but they are usually undersampled due to deficiencies in the spatial coverage of water level measurements. This study aims to address this issue by investigating the use of airborne lidar measurements to study tidal statistics and river slope in the Columbia River estuary. Eight plane transects over a 12-h period yield at least eight independent measurements of water level at 2.5-km increments over a 65-km stretch of the estuary. These data are fit to a sinusoidal curve and the results are compared to seven in situ gauges. In situ– and lidar-based …

Quef-Like, A Non-Homologous Archaeosine Synthase From The Crenarchaeota, Adriana Bon Ramos, Lide Bao, Ben Turner, Valérie De Crécy-Lagard, Dirk Iwata-Reuyl

Chemistry Faculty Publications and Presentations

Archaeosine (G+) is a structurally complex modified nucleoside ubiquitous to the Archaea, where it is found in the D-loop of virtually all archaeal transfer RNA (tRNA). Its unique structure, which includes a formamidine group that carries a formal positive charge, and location in the tRNA, led to the proposal that it serves a key role in stabilizing tRNA structure. Although G+ is limited to the Archaea, it is structurally related to the bacterial modified nucleoside queuosine, and the two share homologous enzymes for the early steps of their biosynthesis. In the Euryarchaeota, the last step of the archaeosine biosynthetic pathway …

Topological And Thermodynamic Factors That Influence The Evolution Of Small Networks Of Catalytic Rna Species, Jessica Anne Mellor Yeates, Philippe Nghe, Niles Lehman

Chemistry Faculty Publications and Presentations

An RNA-directed recombination reaction can result in a network of interacting RNA species. It is now becoming increasingly apparent that such networks could have been an important feature of the RNA world during the nascent evolution of life on the Earth. However, the means by which such small RNA networks assimilate other available genotypes in the environment to grow and evolve into the more complex networks that are thought to have existed in the prebiotic milieu are not known. Here, we used the ability of fragments of the Azoarcus group I intron ribozyme to covalently self-assemble via genotype-selfish and genotype-cooperative …

Atomic Layer Growth Of Inse And Sb₂Se₃ Layered Semiconductors And Their Heterostructure, Robert Browning, Neal Kuperman, Bill Moon, Raj Solanki

Physics Faculty Publications and Presentations

Metal chalcogenides based on the C–M–M–C (C = chalcogen, M = metal) structure possess several attractive properties that can be utilized in both electrical and optical devices. We have shown that specular, large area films of ^_y-InSe and Sb₂Se₃ can be grown via atomic layer deposition (ALD) at relatively low temperatures. Optical (absorption, Raman), crystalline (X-ray diffraction), and composition (XPS) properties of these films have been measured and compared to those reported for exfoliated films and have been found to be similar. Heterostructures composed of a layer of y-InSe (intrinsically n-type) followed by a layer of …

Shift-Symmetric Configurations In Two-Dimensional Cellular Automata: Irreversibility, Insolvability, And Enumeration, Peter Banda, John S. Caughman Iv, Martin Cenek, Christof Teuscher

Mathematics and Statistics Faculty Publications and Presentations

The search for symmetry as an unusual yet profoundly appealing phenomenon, and the origin of regular, repeating configuration patterns have been for a long time a central focus of complexity science, and physics.

Here, we introduce group-theoretic concepts to identify and enumerate the symmetric inputs, which result in irreversible system behaviors with undesired effects on many computational tasks. The concept of so-called configuration shift-symmetry is applied on two-dimensional cellular automata as an ideal model of computation. The results show the universal insolvability of “non-symmetric” tasks regardless of the transition function. By using a compact enumeration formula and bounding the number …

Spatial Resilience Of Forested Landscapes Under Climate Change And Management, Melissa S. Lucash, Robert M. Scheller, Eric J. Gustafson, Brian R. Sturtevant

Environmental Science and Management Faculty Publications and Presentations

Context: Resilience, the ability to recover from disturbance, has risen to the forefront of scientific policy, but is difficult to quantify, particularly in large, forested landscapes subject to disturbances, management, and climate change.

Objectives: Our objective was to determine which spatial drivers will control landscape resilience over the next century, given a range of plausible climate projections across north-central Minnesota.

Methods: Using a simulation modelling approach, we simulated wind disturbance in a 4.3 million ha forested landscape in north-central Minnesota for 100 years under historic climate and five climate change scenarios, combined with four management scenarios: business …

A Numerical Model Investigation Of The Role Of The Glacier Bed In Regulating Grounding Line Retreat Of Thwaites Glacier, West Antarctica, Michael Scott Waibel

Dissertations and Theses

I examine how two different realizations of bed morphology affect Thwaites Glacier response to ocean warming through the initiation of marine ice sheet instability and associated grounding line retreat. A state of the art numerical ice sheet model is used for this purpose. The bed configurations used are the 1-km resolution interpolated BEDMAP2 bed and a higher-resolution conditional simulation produced by John Goff at the University of Texas using the same underlying data. The model is forced using a slow ramp approach, where melt of ice on the floating side of the grounding line is increased over time, which gently …

Certifying Loop Pipelining Transformations In Behavioral Synthesis, Disha Puri

Dissertations and Theses

Due to the rapidly increasing complexity in hardware designs and competitive time to market trends in the industry, there is an inherent need to move designs to a higher level of abstraction. Behavioral Synthesis is the process of automatically compiling such Electronic System Level (ESL) designs written in high-level languages such as C, C++ or SystemC into Register-Transfer Level (RTL) implementation in hardware description languages such as Verilog or VHDL. However, the adoption of this flow is dependent on designers' faith in the correctness of behavioral synthesis tools.

Loop pipelining is a critical transformation employed in behavioral synthesis process, and …

Analyzing Glacier Surface Motion Using Lidar Data, Jennifer W. Tellig, Craig Glennie, Andrew G. Fountain, David C. Finnegan

Geology Faculty Publications and Presentations

Understanding glacier motion is key to understanding how glaciers are growing, shrinking, and responding to changing environmental conditions. In situ observations are often difficult to collect and offer an analysis of glacier surface motion only at a few discrete points. Using light detection and ranging (LiDAR) data collected from surveys over six glaciers in Greenland and Antarctica, particle image velocimetry (PIV) was applied to temporally-spaced point clouds to detect and measure surface motion. The type and distribution of surface features, surface roughness, and spatial and temporal resolution of the data were all found to be important factors, which limited the …

The Effects Of Scale Variation On Single-Family Residential Water Use In Portland, Or, Matthew Ryan Lee Bonnette

Dissertations and Theses

With growing urban populations and increasing concerns over the effects of climate change on water supplies, there has recently been a significant amount of interdisciplinary research focused on identifying the drivers of urban water use. Due to unavailability of individual or household level data, these studies are often limited to using spatially aggregated data. There is concern that this aggregation of data may be leading to misrepresentations of the drivers of urban water use, yet there have been few studies that have addressed this concern. As in all spatial quantitative analyses, studies in this area should consider how the spatial …

An Afm-Sims Nano Tomography Acquisition System, Richard William Swinford

Dissertations and Theses

An instrument, adding the capability to measure 3D volumetric chemical composition, has been constructed by me as a member of the Sánchez Nano Laboratory. The laboratory's in situ atomic force microscope (AFM) and secondary ion mass spectrometry systems (SIMS) are functional and integrated as one instrument. The SIMS utilizes a Ga focused ion beam (FIB) combined with a quadrupole mass analyzer. The AFM is comprised of a 6-axis stage, three coarse axes and three fine. The coarse stage is used for placing the AFM tip anywhere inside a (13x13x5 mm³) (xyz) volume. Thus the tip can be moved …

Computational Algorithms For Improved Representation Of The Model Error Covariance In Weak-Constraint 4d-Var, Jeremy A. Shaw

Dissertations and Theses

Four-dimensional variational data assimilation (4D-Var) provides an estimate to the state of a dynamical system through the minimization of a cost functional that measures the distance to a prior state (background) estimate and observations over a time window. The analysis fit to each information input component is determined by the specification of the error covariance matrices in the data assimilation system (DAS). Weak-constraint 4D-Var (w4D-Var) provides a theoretical framework to account for modeling errors in the analysis scheme. In addition to the specification of the background error covariance matrix, the w4D-Var formulation requires information on the model error statistics and …